[modeller_usage] Re: Average the models

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 10/21/24 2:28 AM, Marco Sette via modeller_usage wrote:
> I have obtained five models of a protein with Modeller and I am 
> analyzing them in relation to the wt. There are of course small 
> deviations, and such differences affect some physical properties. In 
> your opinion, should I analyze the separate models or I can take the 
> average structure? In NMR, people often use an average structure so I 
> wonder if it makes sense in the modelling field.

Normally we look at the individual models. If you do want to average the 
structures, I would recommend you at least relax the final structure. 
One way to do that is to use AutoModel.cluster() as per
https://salilab.org/modeller/10.5/manual/node71.html
which does a basic conjugate gradients minimization.

	Ben Webb, Modeller Caretaker
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